Sisko had been married to Sarah Sisko; unknown to him at the time, however, Sarah's body had been occupied by a Prophet to see that their Emissary was born. When the Prophet left Sarah a year after Benjamin was born, Sarah left as well. After her disappearance and ultimate death, Joseph Sisko remarried and had at least three other children with his new wife: Judith and at least two other boys. (DS9: "Image in the Sand")

At some point, he became gravely ill; this was very traumatic for Benjamin. (DS9: "The Alternate") Joseph subsequently recovered, however, receiving several artificial organs.

After the Dominion bombing at Antwerp, his son, grandson and Odo traveled to Earth. Shortly after, Starfleet authorities on Earth, with assistance from Benjamin Sisko and Odo, made it mandatory for the families of all Starfleet officers to undergo blood screenings. He resisted this and complained that his freedoms were being usurped by the government. (DS9: "Homefront", "Paradise Lost")

In 2374, Joseph was very distraught to learn that Jake was the only Federation citizen to remain on Deep Space 9 following the Dominion occupation. He urged Ben to go rescue his son, though Ben reminded his father that during a time of war, that was not his choice to make. (DS9: "A Time to Stand")

Following the murder of Jadzia Dax and the disappearance of the Bajoran wormhole, Benjamin was despondent and grief-stricken over the loss of his friend. Consequently, he moved into his father's home and took to assisting his father in the running of his restaurant. It was here that Ben had visions of a Sarah Sisko. Although he was upset at first, refusing to discuss or acknowledge the identity of the woman Benjamin had seen visions of and subsequently completed a rendering of, Joseph would explain that Sarah was Ben's real mother who left after his birth. Joseph then accompanied his son to Tyree in search of answers as to who Sarah really was and to find the Orb of the Emissary that would release the prophets and re-activate the Wormhole. (DS9: "Image in the Sand", "Shadows and Symbols")

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Joseph Sisko was played by Brock Peters. On the photograph seen in the episode "Image in the Sand", he was portrayed by an unknown actor.

Joseph Sisko was first mentioned by Benjamin in DS9's premiere episode, "Emissary", in the past tense with the statement "My father was a gourmet chef." Both this and Benjamin's recounting of his grave illness in "The Alternate" suggested the elder Sisko was deceased at that point, before "Homefront" revealed him to be alive, if not in the best of health, an element which may have been a nod to "The Alternate".

The line in "Emissary" may also be interpreted as Joseph having given up cooking at some point before opening Sisko's Creole Kitchen, or it may have been that details of the Joseph Sisko character had simply not yet been developed.